e-Spect: In silica spectroscopy of complex molecular systems

Theoretical simulations are essential for the microscopic understanding of spectroscopic data that enable the design of biomarkers and materials. Modeling these complex systems requires a combination of molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) approaches. The development of a fast HPC-driven quantum modeling will give access to spectroscopic response signals. To be able to use this data we will develop methods that support a linked exploration of 3D molecular representations and aggregated statistical measures to enable the user to effectively find spatio-temporal statistical patterns. We will develop method for real-time aggregation of properties from large highly dynamical time series. This allows, e.g,. for the identification of biomarker binding sites in amyloid protein fibrils that enable early-stage detection of Alzheimer’s and related diseases. To ensure the flexibility of the tool a high-level semantic descriptor language will be developed to specify molecular properties of interest used for interactive filtering. Impact:

  1. Provision of a microscopic understanding of biomarkers in Alzheimer’s research
  2. Publish an open-source software for theoretical spectroscopy combined with visual analysis. Since, there exists no scalable software for quantum molecular modeling on PDC’s Cray cluster, our work will benefit the entire international community of computational chemists using contemporary HPC resources
  3. Development of a production level software for molecular animations and scientific storytelling

External funding and synergies: This project has synergies with running projects: (i) EU Horizon 2020 Training Network (ITN) “Theoretical network for computational spectroscopy in natural sciences and engineering (COSINE)”; (ii) Swedish Research Council projects “Light–matter interactions in complex molecular systems as studied by novel response theory approaches” (iii) MolDome KAW funded projectthat will develop animations and real-time complex animations used in science communication in dome theaters as well as in class room teaching.